Re: [Apbs-users] ERROR: initAPOL: Got NULL Vparam object!

[Vigneshwar R. <vms...@gm...>]

Thanks again, Dr. Baker.

I will have to check why my calculations take so much time.

The parameters I chose are the suggested values from your PNAS article and
from the discussions in the APBS user list. They are:

         grid 0.1 0.1 0.1
        mol 1
        srfm sacc
        swin 0.3
        srad 1.4
        press 0.2394
        gamma 0.0209
        bconc 0.03348
        sdens 10.0
        dpos 0.2
        temp 300.00
        calcenergy total
        calcforce no

Do you think I must optimize these parameters for my system (protein-DNA
complex; ~9000 atoms) by benchmarking it against explicit solvent
calculations?

Will be grateful for any suggestions or pointers.

Thank you,
Sincerely,
Vignesh

On Mon, Nov 29, 2010 at 1:53 AM, Baker, Nathan <Nat...@pn...> wrote:

> Hi Vignesh --
>
> There shouldn't be a huge difference in time; the computational complexity
> for the SAV and WCA calculations is approximately linear.
>
> The energy differences likely arise from the parameters you've chosen for
> gamma, pressure, and the probe radius.  How did you select these parameters?
>
> Thanks,
>
> --
> Nathan Baker
> Pacific Northwest National Laboratory
> (509) 375-3997
> ________________________________________
> From: Vigneshwar Ramakrishnan [vms...@gm...]
> Sent: Saturday, November 27, 2010 5:56 PM
> To: Baker, Nathan
> Cc: apb...@li...
> Subject: Re: [Apbs-users] ERROR: initAPOL: Got NULL Vparam object!
>
> Thanks, Dr. Baker.
>
> May I please also ask if including the WCA energy calculation will take
> enormous time ?
> I did a test calculation with ~800 atoms and it took about 1.5 hours.
> Another calculation with ~9000 atoms has been running for about ~15 hours
> now and has not yet ended. I just want to know if I am right, or I have made
> some mistake somewhere unknowingly.
>
> Also, for the 800 atom system, the total apolar energy is about ~2000
> kJ/mol with WCA model and ~3000 kJ/mol with the SAV model (that is, only
> gamma and press keywords; bconc set to 0). Can I please check with you if
> such a huge difference is expected (1000kJ/mol)? From the PNAS article  (
> http://www.pnas.org/content/103/22/8331.full) I understand that the SAV
> model significantly brings the apolar solvation energies closer to the
> explicit solvent calculations. If the SAV model is accurate enough (despite
> the large difference introduced by WCA model), then, in light of the
> time-consuming nature of the WCA calculations, can I rely just on the
> calculations based on the SAV model? (I am interested in calculating the
> relative binding energies of the wild type and mutant protein-DNA system.)
>
> I will be glad to for any pointers and suggestions.
>
> Thanks very much,
> Sincerely,
> Vignesh
>
>
>
> On Sat, Nov 27, 2010 at 11:30 PM, Baker, Nathan <Nat...@pn...
> <mailto:Nat...@pn...>> wrote:
> Great; I'm glad it's fixed!
>
> --
> Pacific Northwest National Laboratory
> (509) 375-3997
> ________________________________________
> From: Vigneshwar Ramakrishnan [vms...@gm...<mailto:
> vms...@gm...>]
> Sent: Saturday, November 27, 2010 12:08 AM
> To: apb...@li...<mailto:
> apb...@li...>
> Subject: Re: [Apbs-users] ERROR: initAPOL: Got NULL Vparam object!
>
> Dear All,
>
> Sorry, I realized that this error was because I hadn't given the parameter
> file. The latest version (1.3) gave me the detailed error.
>
> Thanks very much,
> Vignesh
>
> On Fri, Nov 26, 2010 at 8:04 PM, Vigneshwar Ramakrishnan <
> vms...@gm...<mailto:vms...@gm...><mailto:
> vms...@gm...<mailto:vms...@gm...>>> wrote:
> Dear All,
>
> I am trying to calculate the nonpolar contribution for a protein-DNA system
> and I got the following error. I am attaching the input file that I used as
> well. Could you please give me some pointers as to what this error means?
> Thanks very much.
>
> Parsed input file.
> Got paths for 3 molecules
> Reading PQR-format atom data from mon1.pqr.
>  8222 atoms
>  Centered at (4.971e+01, 4.898e+01, 5.001e+01)
>  Net charge -4.00e+00 e
> Reading PQR-format atom data from mon2.pqr.
>  828 atoms
>  Centered at (4.215e+01, 3.732e+01, 4.989e+01)
>  Net charge -2.40e+01 e
> Reading PQR-format atom data from comp.pqr.
> initAPOL:  Got NULL Vparam object!
> Error calculating apolar solvation quantities!
>  9050 atoms
>  Centered at (4.971e+01, 4.898e+01, 5.001e+01)
>  Net charge -2.80e+01 e
> Preparing to run 3 PBE calculations.
> ----------------------------------------
> CALCULATION #1 (mol1): APOLAR
> finished processing 0
>
>
> ----------------------------------------------------------------------
>
> Sincerely,
> Vignesh
>
>
> --
> R.Vigneshwar
> Graduate Student,
> Dept. of Chemical & Biomolecular Engg,
> National University of Singapore,
> Singapore
>
> "Strive for Excellence, Never be satisfied with the second Best!!"
>
> I arise in the morning torn between a desire to improve the world and a
> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
>
>
>
> --
> R.Vigneshwar
> Graduate Student,
> Dept. of Chemical & Biomolecular Engg,
> National University of Singapore,
> Singapore
>
> "Strive for Excellence, Never be satisfied with the second Best!!"
>
> I arise in the morning torn between a desire to improve the world and a
> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
>
>
>
> --
> R.Vigneshwar
> Graduate Student,
> Dept. of Chemical & Biomolecular Engg,
> National University of Singapore,
> Singapore
>
> "Strive for Excellence, Never be satisfied with the second Best!!"
>
> I arise in the morning torn between a desire to improve the world and a
> desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
>



-- 
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

I arise in the morning torn between a desire to improve the world and a
desire to enjoy the world. This makes it hard to plan the day. (E.B. White)